GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Caldicellulosiruptor hydrothermalis 108

Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_013402102.1 CALHY_RS00635 class II fructose-bisphosphate aldolase

Query= SwissProt::P13243
         (285 letters)



>NCBI__GCF_000166355.1:WP_013402102.1
          Length = 278

 Score =  192 bits (487), Expect = 9e-54
 Identities = 110/286 (38%), Positives = 163/286 (56%), Gaps = 16/286 (5%)

Query: 3   LVSMTEMLNTAKEKGYAVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGGFKT 62
           LV++ E+L+  K K + VG FN  + +F + ++ AAE+ + P+I+GV++   R++     
Sbjct: 2   LVNLNEVLSYTKVKKFGVGMFNGLSADFYEGLIDAAEQLRCPIIIGVAD---RFVDRLDF 58

Query: 63  VVAMVKALMEEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVATTAK 122
            +     +    + +VPV +HLDH  S ++  +AI AGFTSVM D S  PFEEN+  T +
Sbjct: 59  EMIAEVMIFLAKRASVPVCVHLDHAKSLKNIMRAIKAGFTSVMFDGSSLPFEENIKRTKE 118

Query: 123 VVELAHFHGVSVEAELGTVGGQEDDVIAEGVIYADPKECQELVERTGIDCLAPALGSVHG 182
           +VE+AH  GVSVE ELG VG  + D       Y  P E +E  ++T +D LA ++G+VHG
Sbjct: 119 IVEIAHSVGVSVEGELGVVGRGDFD-FKNPEFYTKPDEAEEFAQKTQVDALAVSIGTVHG 177

Query: 183 PYKGEPNLGFKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGTAKINVNTENQISSAK 242
            YKGEP L F+ + EI K     LVLHGG+G+   D KK I  G  K+N+ T+  ++   
Sbjct: 178 VYKGEPKLDFERLSEIRKRVDCYLVLHGGSGLSDEDFKKCIEYGINKVNIFTDLTLAINA 237

Query: 243 AVRETLAAKPDEYDPRKYLGPA-----REAIKETVIGKMREFGSSN 283
            + E +    D       L PA     RE +K+  I K++ FGS N
Sbjct: 238 QLPEFIKQTED-------LTPAIFEKIREIVKQEAIKKLKIFGSYN 276


Lambda     K      H
   0.313    0.131    0.367 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 211
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 285
Length of database: 278
Length adjustment: 26
Effective length of query: 259
Effective length of database: 252
Effective search space:    65268
Effective search space used:    65268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory